The story was nothing like IX's story so the idea that it does anything to 'tarnish' it is a ridiculous notion.
Other than Alexandria's architecture and loose history(that does not even line up with IX's in the first place before things 'changed') the closest thing is Otis(Ortis?) being a somewhat Steiner character and even that is far removed, that's already more than Sphene's similarities to Garnet.
It's clearly done that way so it can be its own thing than a rehash of IX's story which wouldn't fit and would confuse players who haven't played IX, the story itself didn't even try to be anything like IX.